**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Fri Jan 10 2014 - 16:20:45 CST

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Orientation has quaternion values on the 4-dimensional unit sphere, and the

distance between two different orientations is the angle between the two

quaternions on that sphere (in radians). Because of symmetry a quaternion

and its opposite are the same rotation so a 30¡Æ rotation will be 15¡Æ away

from the quaternion that represents the identity (convert in radians of

course).

See the following paper and the Coutsias reference therein:

http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.813594

Bests

Giacomo

On Jan 9, 2014 7:28 PM, "¼¿ëÀÏ" <seoyi86_at_gmail.com> wrote:

*> Fiorin, I'm sorry that my mistake. I want to know unit of width, not
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*> "tilt" but "orientation".
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*>
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*> colvar {
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*> name Rotation_ring
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*>
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*> width 1.0 <-- what is unit of width?
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*>
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*> orientation {
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*> atoms {
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*> psfSegID 8RA
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*> atomNameResidueRange CA 1 - 8
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*> }
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*> refPositionsFile ../lt8mer.all.colvars.namd.coor
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*> refPositionsCol B
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*> }
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*> }
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*>
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*> Yongil
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*>
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*>
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*> 2014/1/9 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
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*>
*

*>> Yongil, the "tilt" variable is the cosine of the tilt angle. So the
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*>> whole interval of values is -1 to 1. Cos(0) = 1.00 and cos(30) = 0.86, so
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*>> you want the width to be small enough to distinguish well between those two
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*>> values (e.g. width = 0.01).
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*>>
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*>> Giacomo
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*>>
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*>>
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*>> On Thu, Jan 9, 2014 at 3:27 AM, ¼¿ëÀÏ <seoyi86_at_gmail.com> wrote:
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*>>
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*>>> Dear NAMD users
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*>>>
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*>>> Hi, I'm using orientation component in colvars module for control of
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*>>> protein's tilt angle.
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*>>> I try to rotation of protein's tilt angle from 0 degree to 30 degree.
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*>>> But, I don't know value of width in orientation either degree or radian--089e012940d830dadb04efa523a7--
*

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